New module: nanoq

modules/nf-core/nanoq/environment.yml

@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "nanoq"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::nanoq=0.10.0"

modules/nf-core/nanoq/main.nf

@@ -0,0 +1,74 @@
+process NANOQ {
+
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/nanoq:0.10.0--h031d066_2' :
+        'biocontainers/nanoq:0.10.0--h031d066_2'}"
+
+    input:
+    tuple val(meta), path(ontreads)
+    val(output_type) // u: uncompressed; b: Bzip2; g: Gzip; l: Lzma
+
+    output:
+    tuple val(meta), path("*.stats")                                                  , emit: stats
+    tuple val(meta), path("*")                                                        , emit: reads
+    path "versions.yml"                                                               , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def seq_type = ontreads.baseName.split("\\.")[1]
+
+    if (output_type == 'u') {
+        output_ext = ""
+    } else if (output_type == 'b') {
+        output_ext = ".bz2"
+    } else if (output_type == 'g') {
+        output_ext = ".gz"
+    } else if (output_type == 'l') {
+        output_ext = ".lzma"
+    }
+
+    """
+    nanoq -i $ontreads \\
+        -r ${prefix}.stats \\
+        -O $output_type \\
+        -o ${prefix}_nanoq.${seq_type}${output_ext}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        nanoq: \$(nanoq --version | sed -e 's/nanoq //g')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def seq_type = ontreads.baseName.split("\\.")[1]
+    if (output_type == 'u') {
+        output_ext = ""
+    } else if (output_type == 'b') {
+        output_ext = ".bz2"
+    } else if (output_type == 'g') {
+        output_ext = ".gz"
+    } else if (output_type == 'l') {
+        output_ext = ".lzma"
+    }
+
+    """
+    touch ${prefix}_nanoq.${seq_type}${output_ext}
+    touch ${prefix}.stats
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        nanoq: \$(nanoq --version | sed -e 's/nanoq //g')
+    END_VERSIONS
+    """
+}

modules/nf-core/nanoq/meta.yml

@@ -0,0 +1,61 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "nanoq"
+description: Nanoq implements ultra-fast read filters and summary reports for high-throughput nanopore reads.
+keywords:
+  - nanoq
+  - Read filters
+  - Read trimming
+  - Read report
+tools:
+  - "nanoq":
+      description: "Ultra-fast quality control and summary reports for nanopore reads"
+      homepage: "https://github.com/esteinig/nanoq"
+      documentation: "https://github.com/esteinig/nanoq"
+      tool_dev_url: "https://github.com/esteinig/nanoq"
+      doi: "10.21105/joss.02991"
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - ontreads:
+      type: file
+      description: Compressed or uncompressed nanopore reads in fasta or fastq formats.
+      pattern: "*.{fa,fna,faa,fasta,fq,fastq}{,.gz,.bz2,.xz}"
+
+  - output_type:
+      type: string
+      description: "Specifies the output compression type: 'b' for Bzip2, 'g' for gzip, 'l' for Lzma, and 'u' for uncompressed."
+      pattern: "*.{fa,fna,faa,fasta,fq,fastq}{,.gz,.bz2,.lzma}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - stats:
+      type: file
+      description: Summary report of reads statistics.
+      pattern: "*.stats"
+
+  - reads:
+      type: file
+      description: Filtered reads.
+      pattern: "*.{fa,fna,faa,fasta,fq,fastq}{,.gz,.bz2,.lzma}"
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@LilyAnderssonLee"
+maintainers:
+  - "@LilyAnderssonLee"

modules/nf-core/nanoq/tests/main.nf.test

@@ -0,0 +1,122 @@
+nextflow_process {
+
+    name "Test Process NANOQ"
+    script "../main.nf"
+    process "NANOQ"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "nanoq"
+
+    test("sarscov2 - nanopore_uncompressed") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true ], // meta map
+                    file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
+                ]
+
+                input[1] = 'u'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - nanopore_compressed_gz") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true ], // meta map
+                    file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
+                ]
+                input[1] = 'g'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+    test("sarscov2 - nanopore_uncompressed_bz2") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true ], // meta map
+                    file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
+                ]
+                input[1] = 'b'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+    test("sarscov2 - nanopore_uncompressed_lzma") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true ], // meta map
+                    file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
+                ]
+                input[1] = 'l'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - nanopore - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true ], // meta map
+                    file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
+                    ]
+                    input[1] = 'g'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+}